How can drawing response curves for NGS gene expression PE sample trimming options ?

Question

[Ahmad]

I have NGS gene expression PE sample and I want to study and assess the effect of these trimming options like length of the sliding window, number of mismatches for alignment seeds of illuminaclip and alignment score of illuminaclip. I will repeat the analysis at 5 different values and draw response curves. My question is how can draw response curves?

[lieven.sterck]

your idea is not bad but I do wonder if all these have not been investigated before. Did you went through the literature to see if there are no papers on this specific topic?

On the other hand, these things should not have too much effect on the final expression result (given that you don't run them with crazy thersholds ...)